I admit I'm still grappling with the physics for quantum computers :(
But is what you're saying with quantum decoherence also the reason why the qubit state only has a very short lifetime in practical quantum computers? Therefore once you have programmed your qubits you need to get the result out fast before the states become damaged.
You need to find a way to keep the qubit a qubit and not getting it reduced to a normal bit. This is the complex part as this means fighting decoherence.